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Sequencing Haiti's Cholera Epidemic

Rapid DNA sequencing identifies the origins of the cholera outbreak.

December 10, 2010

According to the most detailed genetic analysis yet of the strain of cholera bacteria infecting people in Haiti, the pathogen most likely originated in South Asia rather than the Caribbean or Latin America. While scientists still don’t know exactly how the bacteria made its way to Haiti, the findings suggest it must have been introduced by human activity. They also lend new urgency to public health efforts; the South Asian strain is both more virulent and more resistant to antibiotic drugs than those currently circulating in Latin America. Since the outbreak began in October, 93,000 people have become sick and more than 2,000 have died.

Eric Schadt and collaborators at Pacific Biosciences, a sequencing company that has developed a novel method for rapidly reading single molecules of DNA, sequenced and analyzed the microbes’ DNA in just two days. The ability to quickly analyze pathogens is essential if it is to aid public health responses.

According to a release from Pacific Biosciences, which raised $200 million in an initial public offering last month, researchers sequenced five different cholera strains sent from Harvard Medical School: two samples from the current Haiti outbreak, two samples from South Asia (Bangladeshi isolates from 1971 and 2008), and one sample from Latin America (a 1991 Peruvian isolate). The team then compared this high resolution whole genome sequence information to DNA sequence information available in public databases for 23 diverse strains of V. cholerae. The research was published online this week in the New England Journal of Medicine.

The implications of the appearance of this strain are worrisome: as compared with many cholera strains, it is associated with increased virulence, enhanced ability to survive in the environment and in a human host, and increased antibiotic resistance. These factors have substantial epidemiologic ramifications for the entire region and implications for optimal public health approaches to arresting the epidemic’s spread.

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